EpiCompare compares different epigenetic datasets for benchmarking and quality control purposes. The report consists of three main sections:
Input peak files. Total of 2 samples:
## [1] "File1: CnR"
## [1] "File2: CnT"
This information is displayed only if summary metrics from Picard is provided. See help manual.
| Sample | PeakN before tidy | Blacklisted peaks removed (%) | Non-standard peaks removed (%) | PeakN after tidy |
|---|---|---|---|---|
| CnR | 2707 | 6.10 | 0 | 2542 |
| CnT | 1670 | 5.39 | 0 | 1580 |
Distribution of peak widths in each sample after tidying.
Heatmap of percentage overlaps between input peak files. Hover over the heatmap for percentage values.
The plot is displayed only if a reference peak file is provided and stat_plot = TRUE. Depending on the format of the reference file, the function output different plots:
ChromHMM annotates different chromatin states (ChromHMM). The annotation used were obtained from here.
ChromHMM annotation of individual peak files.
ChromHMM annotation of sample peaks found in reference peaks.
ChromHMM annotation of reference peaks found in sample peaks.
ChromHMM annotation of sample peaks not found in reference peaks.
ChromHMM annotation of reference peaks not found in sample peaks.